I would use
find -name \*.avi -exec git annex add {} \;
but other than that, this seems fine. Depending on your level of OCD,
it might make sense to throw away the initial repo once your data is
clean and import everything in a clean one. That's what I do.
Richard
PS: There are various tools for finding duplicates, but git-annex
gives you this functionality for free, so..